myboard.c

From
imx_iomux_v3_setup_pad(MX6_PAD_CSI0_DAT10__UART1_TX_DATA | UART_PAD_CTRL);
imx_iomux_v3_setup_pad(MX6_PAD_CSI0_DAT11__UART1_RX_DATA | UART_PAD_CTRL);

To
imx_iomux_v3_setup_pad(MX6_PAD_EIM_D24__UART3_TX_DATA | UART_PAD_CTRL);
imx_iomux_v3_setup_pad(MX6_PAD_EIM_D25__UART3_RX_DATA | UART_PAD_CTRL);

myboard.h

From
#define CONFIG_MXC_UART_BASE  UART1_BASE
#define CONFIG_CONSOLE_DEV    "ttymxc0"
TO
#define CONFIG_MXC_UART_BASE UART3_BASE
#define CONFIG_CONSOLE_DEV "ttymxc2"

mx6q_pins.h

MX6_PAD_DECL(EIM_D24__UART3_TX_DATA, 0x03C8, 0x00B4, 2, 0x0000, 0, 0)
MX6_PAD_DECL(EIM_D25__UART3_RX_DATA, 0x03CC, 0x00B8, 2, 0x0930, 1, 0)

This is where I somehow need to change from GPIO4 to GPIO5 for IO9 and GPIO6 for IO10 I think

MX6_PAD_DECL(KEY_ROW1__GPIO4_IO09, 0x05D4, 0x0204, 5, 0x0000, 0, 0)
MX6_PAD_DECL(KEY_COL2__GPIO4_IO10, 0x05D8, 0x0208, 5, 0x0000, 0, 0)